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Alan Orth 2023-01-22 21:53:45 +03:00
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122
content/posts/2023-01.md
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@ -285,4 +285,126 @@ Total number of bot hits purged: 4027
- Export entire CGSpace to check Initiative mappings, and add nineteen...
- Start a harvest on AReS
## 2023-01-18
- I'm looking at all the ORCID identifiers in the database, which seem to be way more than I realized:
```console
localhost/dspacetest= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=247) to /tmp/2023-01-18-orcid-identifiers.txt;
COPY 4231
$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/2023-01-18-orcid-identifiers.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2023-01-18-orcids.txt
$ wc -l /tmp/2023-01-18-orcids.txt
4518 /tmp/2023-01-18-orcids.txt
```
- Then I resolved them from ORCID and updated them in the database:
```console
$ ./ilri/resolve-orcids.py -i /tmp/2023-01-18-orcids.txt -o /tmp/2023-01-18-orcids-names.txt -d
$ ./ilri/update-orcids.py -i /tmp/2023-01-18-orcids-names.txt -db dspace -u dspace -p 'fuuu' -m 247
```
- Then I updated the controlled vocabulary
- CGSpace became inactive in the afternoon, with a high number of locks, but surprisingly low CPU usage:
```console
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
83 dspaceApi
7829 dspaceWeb
```
- In the DSpace logs I see some weird SQL messages, so I decided to restart PostgreSQL and Tomcat 7...
- I hope this doesn't cause some issue with in-progress workflows...
- I see another user on Cox in the US (98.186.216.144) crawling and scraping XMLUI with Python
- I will add python to the list of bad bot user agents in nginx
- While looking into the locks I see some potential Java heap issues
- Indeed, I see two out of memory errors in Tomcat's journal:
```console
tomcat7[310996]: java.lang.OutOfMemoryError: Java heap space
tomcat7[310996]: Jan 18, 2023 1:37:03 PM org.apache.tomcat.jdbc.pool.ConnectionPool abandon
```
- Which explains why the locks went down to normal numbers as I was watching... (because Java crashed)
## 2023-01-19
- Update a bunch of ORCID identifiers, Initiative mappings, and regions on CGSpace
- So it seems an IFPRI user got caught up in the blocking I did yesterday
- Their ISP is Comcast...
- I need to re-work the ASN blocking on nginx, but for now I will just get the ASNs again minus Comcast:
```console
$ wget https://asn.ipinfo.app/api/text/list/AS714 \
https://asn.ipinfo.app/api/text/list/AS16276 \
https://asn.ipinfo.app/api/text/list/AS15169 \
https://asn.ipinfo.app/api/text/list/AS23576 \
https://asn.ipinfo.app/api/text/list/AS24940 \
https://asn.ipinfo.app/api/text/list/AS13238 \
https://asn.ipinfo.app/api/text/list/AS32934 \
https://asn.ipinfo.app/api/text/list/AS14061 \
https://asn.ipinfo.app/api/text/list/AS12876 \
https://asn.ipinfo.app/api/text/list/AS55286 \
https://asn.ipinfo.app/api/text/list/AS203020 \
https://asn.ipinfo.app/api/text/list/AS204287 \
https://asn.ipinfo.app/api/text/list/AS50245 \
https://asn.ipinfo.app/api/text/list/AS6939 \
https://asn.ipinfo.app/api/text/list/AS16509 \
https://asn.ipinfo.app/api/text/list/AS14618
$ cat AS* | sort | uniq | wc -l
18179
$ cat /tmp/AS* | ~/go/bin/mapcidr -a > /tmp/networks.txt
$ wc -l /tmp/networks.txt
5872 /tmp/networks.txt
```
## 2023-01-20
- A lot of work on CGSpace metadata (ORCID identifiers, regions, and Initiatives)
- I noticed that MEL and CGSpace are using slightly different vocabularies for SDGs so I sent an email to Salem and Sara
## 2023-01-21
- Export the Initiatives community again to perform collection mappings and country/region fixes
## 2023-01-22
- There has been a high load on the server for a few days, currently 8.0... and I've been seeing some PostgreSQL locks stuck all day:
```console
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
11 dspaceApi
28 dspaceCli
981 dspaceWeb
```
- Looking at the locks I see they are from this morning at 5:00 AM, which is the `dspace checker-email` script
- Last week I disabled the one that ones at 4:00 AM, but I guess I will experiment with disabling this too...
- Then I killed the PIDs of the locks
```console
$ psql -c "SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid WHERE application_name='dspaceCli';" | less -S
...
$ ps auxw | grep 18986
postgres 1429108 1.9 1.5 3359712 508148 ? Ss 05:00 13:40 postgres: 12/main: dspace dspace 127.0.0.1(18986) SELECT
```
- Also, I checked the age of the locks and killed anything over 1 day:
```console
$ psql < locks-age.sql | grep days | less -S
```
- Then I ran all updates on the server and restarted it...
- Salem responded to my question about the SDG mismatch between MEL and CGSpace
- We agreed to use a version based on the text of [this site](http://metadata.un.org/sdg/?lang=en)
- Salem is having issues with some REST API submission / updates
- I updated DSpace Test with a recent CGSpace backup and created a super admin user for him to test
- Clean and normalize fifty-eight IFPRI records for batch import to CGSpace
- I did a duplicate check and found six, so that's good!
- I exported the entire CGSpace to check for missing Initiative mappings
- Then I exported the Initiatives community to check for missing regions
- Then I ran the script to check for missing ORCID identifiers
- Then *finally*, I started a harvest on AReS
<!-- vim: set sw=2 ts=2: -->

138
docs/2023-01/index.html
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@ -19,7 +19,7 @@ I see we have some new ones that aren&rsquo;t in our list if I combine with this
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-01/" />
<meta property="article:published_time" content="2023-01-01T08:44:36+03:00" />
<meta property="article:modified_time" content="2023-01-15T08:10:16+03:00" />
<meta property="article:modified_time" content="2023-01-17T22:38:55+03:00" />
@ -44,9 +44,9 @@ I see we have some new ones that aren&rsquo;t in our list if I combine with this
"@type": "BlogPosting",
"headline": "January, 2023",
"url": "https://alanorth.github.io/cgspace-notes/2023-01/",
"wordCount": "2250",
"wordCount": "2969",
"datePublished": "2023-01-01T08:44:36+03:00",
"dateModified": "2023-01-15T08:10:16+03:00",
"dateModified": "2023-01-17T22:38:55+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -452,6 +452,138 @@ I see we have some new ones that aren&rsquo;t in our list if I combine with this
<li>Export entire CGSpace to check Initiative mappings, and add nineteen&hellip;</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-01-18">2023-01-18</h2>
<ul>
<li>I&rsquo;m looking at all the ORCID identifiers in the database, which seem to be way more than I realized:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>localhost/dspacetest= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=247) to /tmp/2023-01-18-orcid-identifiers.txt;
</span></span><span style="display:flex;"><span>COPY 4231
</span></span><span style="display:flex;"><span>$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/2023-01-18-orcid-identifiers.txt | grep -oE <span style="color:#e6db74">&#39;[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}&#39;</span> | sort -u &gt; /tmp/2023-01-18-orcids.txt
</span></span><span style="display:flex;"><span>$ wc -l /tmp/2023-01-18-orcids.txt
</span></span><span style="display:flex;"><span>4518 /tmp/2023-01-18-orcids.txt
</span></span></code></pre></div><ul>
<li>Then I resolved them from ORCID and updated them in the database:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ ./ilri/resolve-orcids.py -i /tmp/2023-01-18-orcids.txt -o /tmp/2023-01-18-orcids-names.txt -d
</span></span><span style="display:flex;"><span>$ ./ilri/update-orcids.py -i /tmp/2023-01-18-orcids-names.txt -db dspace -u dspace -p <span style="color:#e6db74">&#39;fuuu&#39;</span> -m <span style="color:#ae81ff">247</span>
</span></span></code></pre></div><ul>
<li>Then I updated the controlled vocabulary</li>
<li>CGSpace became inactive in the afternoon, with a high number of locks, but surprisingly low CPU usage:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ psql -c <span style="color:#e6db74">&#39;SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;&#39;</span> | grep -o -E <span style="color:#e6db74">&#39;(dspaceWeb|dspaceApi|dspaceCli)&#39;</span> | sort | uniq -c
</span></span><span style="display:flex;"><span> 83 dspaceApi
</span></span><span style="display:flex;"><span> 7829 dspaceWeb
</span></span></code></pre></div><ul>
<li>In the DSpace logs I see some weird SQL messages, so I decided to restart PostgreSQL and Tomcat 7&hellip;
<ul>
<li>I hope this doesn&rsquo;t cause some issue with in-progress workflows&hellip;</li>
</ul>
</li>
<li>I see another user on Cox in the US (98.186.216.144) crawling and scraping XMLUI with Python
<ul>
<li>I will add python to the list of bad bot user agents in nginx</li>
</ul>
</li>
<li>While looking into the locks I see some potential Java heap issues
<ul>
<li>Indeed, I see two out of memory errors in Tomcat&rsquo;s journal:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>tomcat7[310996]: java.lang.OutOfMemoryError: Java heap space
</span></span><span style="display:flex;"><span>tomcat7[310996]: Jan 18, 2023 1:37:03 PM org.apache.tomcat.jdbc.pool.ConnectionPool abandon
</span></span></code></pre></div><ul>
<li>Which explains why the locks went down to normal numbers as I was watching&hellip; (because Java crashed)</li>
</ul>
<h2 id="2023-01-19">2023-01-19</h2>
<ul>
<li>Update a bunch of ORCID identifiers, Initiative mappings, and regions on CGSpace</li>
<li>So it seems an IFPRI user got caught up in the blocking I did yesterday
<ul>
<li>Their ISP is Comcast&hellip;</li>
<li>I need to re-work the ASN blocking on nginx, but for now I will just get the ASNs again minus Comcast:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ wget https://asn.ipinfo.app/api/text/list/AS714 <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> https://asn.ipinfo.app/api/text/list/AS16276 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS15169 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS23576 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS24940 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS13238 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS32934 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS14061 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS12876 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS55286 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS203020 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS204287 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS50245 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS6939 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS16509 \
</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS14618
</span></span><span style="display:flex;"><span>$ cat AS* | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>18179
</span></span><span style="display:flex;"><span>$ cat /tmp/AS* | ~/go/bin/mapcidr -a &gt; /tmp/networks.txt
</span></span><span style="display:flex;"><span>$ wc -l /tmp/networks.txt
</span></span><span style="display:flex;"><span>5872 /tmp/networks.txt
</span></span></code></pre></div><h2 id="2023-01-20">2023-01-20</h2>
<ul>
<li>A lot of work on CGSpace metadata (ORCID identifiers, regions, and Initiatives)</li>
<li>I noticed that MEL and CGSpace are using slightly different vocabularies for SDGs so I sent an email to Salem and Sara</li>
</ul>
<h2 id="2023-01-21">2023-01-21</h2>
<ul>
<li>Export the Initiatives community again to perform collection mappings and country/region fixes</li>
</ul>
<h2 id="2023-01-22">2023-01-22</h2>
<ul>
<li>There has been a high load on the server for a few days, currently 8.0&hellip; and I&rsquo;ve been seeing some PostgreSQL locks stuck all day:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ psql -c <span style="color:#e6db74">&#39;SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;&#39;</span> | grep -o -E <span style="color:#e6db74">&#39;(dspaceWeb|dspaceApi|dspaceCli)&#39;</span> | sort | uniq -c
</span></span><span style="display:flex;"><span> 11 dspaceApi
</span></span><span style="display:flex;"><span> 28 dspaceCli
</span></span><span style="display:flex;"><span> 981 dspaceWeb
</span></span></code></pre></div><ul>
<li>Looking at the locks I see they are from this morning at 5:00 AM, which is the <code>dspace checker-email</code> script
<ul>
<li>Last week I disabled the one that ones at 4:00 AM, but I guess I will experiment with disabling this too&hellip;</li>
<li>Then I killed the PIDs of the locks</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ psql -c <span style="color:#e6db74">&#34;SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid WHERE application_name=&#39;dspaceCli&#39;;&#34;</span> | less -S
</span></span><span style="display:flex;"><span>...
</span></span><span style="display:flex;"><span>$ ps auxw | grep <span style="color:#ae81ff">18986</span>
</span></span><span style="display:flex;"><span>postgres 1429108 1.9 1.5 3359712 508148 ? Ss 05:00 13:40 postgres: 12/main: dspace dspace 127.0.0.1(18986) SELECT
</span></span></code></pre></div><ul>
<li>Also, I checked the age of the locks and killed anything over 1 day:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ psql &lt; locks-age.sql | grep days | less -S
</span></span></code></pre></div><ul>
<li>Then I ran all updates on the server and restarted it&hellip;</li>
<li>Salem responded to my question about the SDG mismatch between MEL and CGSpace
<ul>
<li>We agreed to use a version based on the text of <a href="http://metadata.un.org/sdg/?lang=en">this site</a></li>
</ul>
</li>
<li>Salem is having issues with some REST API submission / updates
<ul>
<li>I updated DSpace Test with a recent CGSpace backup and created a super admin user for him to test</li>
</ul>
</li>
<li>Clean and normalize fifty-eight IFPRI records for batch import to CGSpace
<ul>
<li>I did a duplicate check and found six, so that&rsquo;s good!</li>
</ul>
</li>
<li>I exported the entire CGSpace to check for missing Initiative mappings
<ul>
<li>Then I exported the Initiatives community to check for missing regions</li>
<li>Then I ran the script to check for missing ORCID identifiers</li>
<li>Then <em>finally</em>, I started a harvest on AReS</li>
</ul>
</li>
</ul>
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<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
<meta property="og:updated_time" content="2023-01-15T08:10:16+03:00" />
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<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2023-01-15T08:10:16+03:00" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2023-01-15T08:10:16+03:00" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2023-01-15T08:10:16+03:00" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
<meta property="og:updated_time" content="2023-01-15T08:10:16+03:00" />
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<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
<meta property="og:updated_time" content="2023-01-15T08:10:16+03:00" />
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<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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